CONIFER MICROBIOMES IN THE ERA OF REFORESTATION: FROM NURSERY ORIGIN TO FIELD OUTPLANTING

Abstract

Increasing wildfire severity and frequency across western North America has created an urgent need for large-scale reforestation. Forest nurseries play a critical role in meeting this demand by producing millions of conifer seedlings annually. Yet seedlings are not transported alone; they carry diverse microbial communities that may influence seedling health, growth, and establishment after planting. These communities may also harbor latent fungal pathogens with the potential to be introduced into recovering post-fire ecosystems. Despite growing interest in plant microbiomes, no studies have used the same cohort of trees to track the trajectory of conifer-associated microbial communities from nursery to field. This thesis examines microbial community dynamics across the reforestation pipeline from nursery production through early field establishment. Chapter 1 reviews the ecological role of fire in western forests, the history of pathogen movement through plant material, mechanisms of rhizosphere microbiome assembly, microbial dynamics in fire-affected soils, and current knowledge of microbial community dynamics in nursery systems and in outplanted seedlings. Chapter 2 investigates the influence of nursery and host species on the rhizosphere microbiomes of ponderosa pine (Pinus ponderosa) and southwestern white pine (P. strobiformis) seedlings grown in two nurseries. Using ITS2 and 16S amplicon sequencing, fungal and bacterial communities associated with nursery seedlings and their potting mix were characterized. Nursery was the dominant driver of microbial community composition, exceeding the influence of host ii species and demonstrating that nursery environments leave a distinct microbial signature on seedlings prior to outplanting. Chapter 3 follows these seedlings after planting within the Calf Canyon-Hermit’s Peak burn scar in northern New Mexico. Rhizosphere microbial communities were monitored during the first year of establishment and compared with those in bulk soil and in naturally regenerating ponderosa pine. Results demonstrated substantial turnover of fungal and bacterial communities following outplanting, including recruitment of ectomycorrhizal fungi, increased similarity to resident soil communities, and a decline in the abundance of many nursery-origin microorganisms. Collectively, this work demonstrates that nursery environments strongly influence the microbial communities that seedlings carry into reforestation sites, but post-fire soils can still function as an important reservoir of microbes that reshape the communities after planting. These findings contribute to a growing understanding of microbiome dynamics in conifer reforestation systems and highlight the importance of continuing to monitor seedlings after planting.